Enrichment of Z-DNA-Forming Sequences Within Super-Enhancers: A Computational and Population-Based Study by Yulia V. Makus, German A. Ashniev, Alexey V. Orlov, Petr I. Nikitin, Zoia G. Zaitseva, Natalia N. Orlova

“…Super-enhancers (SEs) orchestrate high-level transcription by integrating multiple regulatory elements and signals. …”
Get full text

Experimental Insights and Recommendations for Successfully Performing Cerebral Microdialysis With Hydrophobic Drug Candidates by Julia K. Sundheimer, Julia Benzel, Rémi Longuespée, Jürgen Burhenne, Stefan M. Pfister, Kendra K. Maaß, Max Sauter, Kristian W. Pajtler

“…These compounds exhibited varying degrees of non‐specific binding to the surfaces of the microdialysis apparatus, leading to low recovery rates and substantial carry‐over effects. …”
Get full text

Bioinformatics pipeline to guide late‐onset Alzheimer's disease (LOAD) post‐GWAS studies: Prioritizing transcription regulatory variants within LOAD‐associated regions by Michael W. Lutz, Ornit Chiba‐Falek

“…Discussion This study provides a framework to catalogue noncoding variations in enhancers located in LOAD‐GWAS loci and characterize their likelihood to perturb TF binding. The approach integrates multiple data types to characterize and prioritize SNPs for putative regulatory function using single‐cell multi‐omics assays and gene editing.…”
Get full text

miR472 Deficiency Enhances Arabidopsis thaliana Defense Without Reducing Seed Production by Francois Vasseur, Patricia Baldrich, Tamara Jiménez-Góngora, Luis Villar-Martin, Detlef Weigel, Ignacio Rubio-Somoza

“…After having co-existed in plant genomes for at least 200 million years, the products of microRNA (miRNA) and nucleotide-binding leucine-rich repeat protein (NLR) genes formed a regulatory relationship in the common ancestor of modern gymnosperms and angiosperms. …”
Get full text

MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas. by Gaia Rizzo, Mattia Veronese, Paul Expert, Federico E Turkheimer, Alessandra Bertoldo

“…In a previous work we have correlated mRNA maps with the binding patterns of radioligands targeting specific molecular systems and imaged with positron emission tomography (PET) in unrelated control groups. …”
Get full text

Uncovering the molecular mechanisms of Qingdu Zengye Decoction in the treatment of nasopharyngeal carcinoma: an integrative investigation by Qi Quan, Qi Quan, Zeyu Liu, Zeyu Liu, Ran Ding, Yongmiao Lin, Sihe Zhang, Wei Luo, Mengjie Lei, Teng Fan, Teng Fan, Xin Su, Xin Su, Yuanyuan Huang, Yuanyuan Huang, Roujun Peng, Bei Zhang, Bei Zhang

“…Molecular docking was applied to assessed ligand-target binding affinities. Single-cell RNA sequencing (scRNA-seq) was used to analyzed spatial expression patterns in NPC tumor samples.ResultsQZD suppressed tumor progression by inducing apoptosis through modulating Bax in a dose-dependent manner and inhibiting the PI3K-Akt signaling pathway. …”
Get full text

Unlocking the therapeutic potential of unexplored phytocompounds as hepatoprotective agents through integration of network pharmacology and in-silico analysis by Pranali A. Jadhav, Asha B. Thomas, Mohsin K. Pathan, Somdatta Y. Chaudhari, Ravindra D. Wavhale, Sohan S. Chitlange

“…Our findings demonstrate the utility of this integrated approach which transits beyond traditional trial-and-error methods. …”
Get full text

Integration of metabolomic and transcriptomic analyses reveals regulatory functions of the ChREBP transcription factor in energy metabolism by Jie An, Inna Astapova, Guofang Zhang, Andrew L. Cangelosi, Olga Ilkayeva, Hannah Marchuk, Michael J. Muehlbauer, Tabitha George, Joseph Brozinick, Mark A. Herman, Christopher B. Newgard

“…Summary: The transcription factor carbohydrate response element binding protein (ChREBP) activates genes of glucose, fructose, and lipid metabolism in response to carbohydrate feeding. …”
Get full text

Integration of transcriptome and metabolome reveals regulatory mechanisms of volatile flavor formation during tomato fruit ripening by Zhiqiang Liu, Jianxin Wu, Licai Wang, Xiaonan Lu, Golam Jalal Ahammed, Xiaolan Zhang, Xia Cui, Haijing Wang

“…Dual-luciferase assay confirmed the binding of bHLH and AP2/ERF to their structural genes. …”
Get full text

YGL9, encoding the putative chloroplast signal recognition particle 43 kDa protein in rice, is involved in chloroplast development by Zhong-wei WANG, Tian-quan ZHANG, Ya-di XING, Xiao-qin ZENG, Ling WANG, Zhong-xian LIU, Jun-qiong SHI, Xiao-yan ZHU, Ling MA, Yun-feng LI, Ying-hua LING, Xian-chun SANG, Guang-hua HE

Get full text

Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. by Lior Lobel, Nadejda Sigal, Ilya Borovok, Eytan Ruppin, Anat A Herskovits

“…This response was specific and required the nutrient responsive regulator CodY, which is known to bind isoleucine. Further analysis demonstrated that CodY is involved in prfA regulation, playing a role in prfA activation under limiting conditions of BCAAs. …”
Get full text

Anti-Ebola virus mAb 3A6 protects highly viremic animals from fatal outcome via binding GP(1,2) in a position elevated from the virion membrane by Kathryn M. Hastie, Zhe Li Salie, Zunlong Ke, Peter J. Halfmann, Lisa Evans DeWald, Sara McArdle, Ariadna Grinyó, Edgar Davidson, Sharon L. Schendel, Chitra Hariharan, Michael J. Norris, Xiaoying Yu, Chakravarthy Chennareddy, Xiaoli Xiong, Megan Heinrich, Michael R. Holbrook, Benjamin Doranz, Ian Crozier, Yoshihiro Kawaoka, Luis M. Branco, Jens H. Kuhn, John A. G. Briggs, Gabriella Worwa, Carl W. Davis, Rafi Ahmed, Erica Ollmann Saphire

Get full text

De novo design of mIDH1 inhibitors by integrating deep learning and molecular modeling by Dingkang Sun, Lulu Xu, Mengfan Tong, Zhao Wei, Weitong Zhang, Jialong Liang, Xueying Liu, Yuwei Wang

Get full text

Manufacturability and functionality assessment of different formats of T-cell engaging bispecific antibodies by Han Ping Loh, Farouq Bin Mahfut, Serene W Chen, Yuhan Huang, Jianxin Huo, Wei Zhang, Kong Peng Lam, Shengli Xu, Yuansheng Yang

Get full text

Integrative network pharmacology and experimental validation reveal emodin derivatives as potential therapeutics for hepatocellular carcinoma by Wirawan Adikusuma, Firdayani Firdayani, Siska Andrina Kusumastuti, Nuralih Nuralih, Shelvi Listiana, Ayu Masyita, Lalu Muhammad Irham, Siti Hodijah, Suci Zulaikha Hildayani, Eko Mugiyanto

“…Docking simulations were conducted to assess binding affinities, followed by 100 ns MDS to evaluate stability. …”
Get full text

Integrated network toxicology, machine learning and molecular docking reveal the mechanism of benzopyrene-induced periodontitis by Wen Wenjie, Li Rui, Zhuo Pengpeng, Deng Chao, Zhang Donglin

“…Molecular docking demonstrated strong binding affinities between BaP and these targets (binding energies <-5.0 kcal/mol). …”
Get full text

Anti-RBD immunoglobulin levels and their predictive value for SARS-CoV-2 neutralization by Sabine Lichtenegger, Sissy Therese Sonnleitner, Sabine Saiger, Andrea Zauner, Melina Hardt, Barbara Kleinhappl, Gabriel E. Wagner, Ivo Steinmetz

“…This finding has implications for determining possible future correlates of protection.IMPORTANCEThroughout the SARS-CoV-2 pandemic, neutralizing antibody levels have been central to predict a protective immune response. Anti-receptor-binding domain (RBD) enzyme-linked immunosorbent assays (ELISAs) correlate with neutralization assays and are due to the integration of simple performance with timely results used as surrogate assays. …”
Get full text

Molecular mechanism of bisphenols induction of breast cancer through PGR revealed by network toxicology and transcriptomics integration analysis by Baowen Yuan, Yu Li, Jinyuan Chang, Chang Guo, Wei Huang, Yan Wang

“…Molecular docking showed that the PGR protein and five bisphenols had the lowest binding energy (-7.7 ∼ -7.0 kcal/mol) and the highest binding affinity. …”
Get full text

Integrated deep network model with multi-head twofold attention for drug–target interaction prediction by Angelin Jeba P, Tamilpavai G

“…To address these challenges, an integrated deep learning model with Multi-Head Twofold Attention (MHTA) has been proposed for DTI prediction. …”
Get full text

The Toll-like receptor gene family is integrated into human DNA damage and p53 networks. by Daniel Menendez, Maria Shatz, Kathleen Azzam, Stavros Garantziotis, Michael B Fessler, Michael A Resnick

“…Most of the TLR genes respond to p53 via canonical as well as noncanonical promoter binding sites. Importantly, the integration of the TLR gene family into the p53 network is unique to primates, a recurrent theme raised for other gene families in our previous studies. …”
Get full text